DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for next-generation sequencing data

Abstract

The current widespread adoption of next-generation sequencing (NGS) in all branches of basic and clinical genetics fields means that users with highly variable informatics skills, computing facilities and application purposes need to process, analyse, and interpret NGS data. In this landscape, versatility, scalability, and user-friendliness are key characteristics for an NGS analysis tool. We developed DNAscan2, a highly flexible, end-to-end pipeline for the analysis of NGS data, which (i) can be used for the detection of multiple variant types, including SNVs, small indels, transposable elements, short tandem repeats and other large structural variants; (ii) covers all steps of the analysis, from quality control of raw data to the generation of html reports for the interpretation and prioritisation of results; (iii) is highly adaptable and scalable as it can be deployed and run via either a graphic user interface for non-bioinformaticians, a command line tool for personal computer usage, or as a Snakemake workflow that facilitates parallel multi-sample execution for high-performance computing environments; (iv) is computationally efficient by minimising RAM and CPU time requirements. Availability and ImplementationDNAscan2 is implemented in Python3 and is available to download as a command-line tool and graphical-user interface at https://github.com/KHP-Informatics/DNAscanv2 or a Snakemake workflow at https://github.com/KHP-Informatics/DNAscanv2_snakemake.